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@@ -103,7 +103,8 @@ Trust is based on the model's performance on a validation set. After training, w
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on a validation set for each class. If the `ensemble_type` is set to `wmv-f1`, the trust is calculated as 1 + the F1 score.
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If the `ensemble_type` is set to `mv` (the default), the trust is set to 1 for all models.
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3. After a decision has been made for each class independently, the consistency of the predictions with regard to the ChEBI hierarchy
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### Inconsistency correction
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After a decision has been made for each class independently, the consistency of the predictions with regard to the ChEBI hierarchy
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and disjointness axioms is checked. This is
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done in 3 steps:
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- (1) First, the hierarchy is corrected. For each pair of classes $A$ and $B$ where $A$ is a subclass of $B$ (following
@@ -113,7 +114,7 @@ belongs to the direct and indirect superclasses (e.g., primary alcohol, aromatic
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- (2) Next, we check for disjointness. This is not specified directly in ChEBI, but in an additional ChEBI module ([chebi-disjoints.owl](https://ftp.ebi.ac.uk/pub/databases/chebi/ontology/)).
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We have extracted these disjointness axioms into a CSV file and added some more disjointness axioms ourselves (see
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`data>disjoint_chebi.csv` and `data>disjoint_additional.csv`). If two classes $A$ and $B$ are disjoint and we predict
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both, we select one of them randomly and set the other to 0.
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both, we select one of them randomly (https://github.com/ChEB-AI/python-chebifier/issues/6) and set the other to 0.
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- (3) Since the second step might have introduced new inconsistencies into the hierarchy, we repeat the first step, but
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with a small change. For a pair of classes $A \subseteq B$ with predictions $1$ and $0$, instead of setting $B$ to $1$,
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we now set $A$ to $0$. This has the advantage that we cannot introduce new disjointness-inconsistencies and don't have
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